Annotation Categories of the Plasmid Cluster







Summary of the plasmid cluster

Basic Information about the Plasmid Cluster

  Cluster Information   Plasmid Cluster ID   C660
  Reference Plasmid   NZ_CP043485.1
  Reference Plasmid Size   168626
  Reference Plasmid GC Content   0.35
  Reference Plasmid Mobility Type   non-mobilizable





Mutation sites in the plasmid cluster


The table lists mutations identified in the plasmid cluster.
Note: Mutations identified in this plasmid cluster are listed below. Click on a mutation ID to view full details..

mutid gname pos count tissue frequnt biotype consequence impact nucchange aachange
M0170758 JEJANKPH_00137 128412 3 Gut 0.19 protein_coding synonymous_variant LOW 1410G>T Pro470Pro
M0170759 JEJANKPH_00137 128448 3 Gut 0.19 protein_coding missense_variant MODERATE 1374G>T Lys458Asn
M0170760 JEJANKPH_00137 128571 3 Gut 0.19 protein_coding synonymous_variant LOW 1251T>G Thr417Thr
M0170761 JEJANKPH_00137 128574 3 Gut 0.19 protein_coding synonymous_variant LOW 1248A>T Gly416Gly
M0170762 JEJANKPH_00137 128580 3 Gut 0.19 protein_coding synonymous_variant LOW 1242T>C Asp414Asp
M0170763 JEJANKPH_00137 128583 3 Gut 0.19 protein_coding synonymous_variant LOW 1239C>T Thr413Thr
M0170764 JEJANKPH_00137 128586 3 Gut 0.19 protein_coding synonymous_variant LOW 1236A>C Ala412Ala
M0170765 JEJANKPH_00137 128598 3 Gut 0.19 protein_coding synonymous_variant LOW 1224T>C Gly408Gly
M0170766 JEJANKPH_00137 129291 3 Gut 0.19 protein_coding synonymous_variant LOW 531A>G Leu177Leu
M0170767 JEJANKPH_00137 129449 3 Gut 0.19 protein_coding missense_variant MODERATE 373C>G Leu125Val
M0170768 JEJANKPH_00135 129908 3 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -2609T>G None
M0170769 JEJANKPH_00138 131221 3 Gut 0.19 protein_coding missense_variant MODERATE 1216G>A Ala406Thr
M0170770 JEJANKPH_00138 131278 3 Gut 0.19 protein_coding synonymous_variant LOW 1273C>T Leu425Leu
M0170771 JEJANKPH_00138 131323 3 Gut 0.19 protein_coding missense_variant MODERATE 1318A>T Met440Leu
M0170772 JEJANKPH_00138 131334 3 Gut 0.19 protein_coding synonymous_variant LOW 1329A>G Leu443Leu
M0170773 JEJANKPH_00138 131868 3 Gut 0.19 protein_coding synonymous_variant LOW 1863A>G Val621Val
M0170774 JEJANKPH_00136 133219 3 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -4839C>T None
M0170775 JEJANKPH_00136 133260 3 Gut 0.19 protein_coding upstream_gene_variant MODIFIER -4880A>G None
M0170776 JEJANKPH_00140 133641 3 Gut 0.19 protein_coding missense_variant MODERATE 1064T>C Leu355Pro
M0170777 JEJANKPH_00140 133721 3 Gut 0.19 protein_coding synonymous_variant LOW 984T>C His328His
M0170778 JEJANKPH_00140 133982 3 Gut 0.19 protein_coding missense_variant MODERATE 723T>G Phe241Leu
M0170779 JEJANKPH_00140 134221 3 Gut 0.19 protein_coding missense_variant MODERATE 484T>C Cys162Arg
M0170780 JEJANKPH_00140 134286 3 Gut 0.19 protein_coding missense_variant MODERATE 419G>A Gly140Glu
M0170781 JEJANKPH_00020 18222 3 Gut 0.19 protein_coding synonymous_variant LOW 567C>T Asp189Asp
M0170782 JEJANKPH_00020 18257 3 Gut 0.19 protein_coding synonymous_variant LOW 532C>T Leu178Leu






Analysis of virulence factors contributing to bacterial pathogenicity


This table presents virulence factors identified within the plasmid cluster.
      Note: Virulence factor analysis was performed using VFDB. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known virulence factors are listed.

Gene Name vf_gene_id vf_name identity evalue qstart qend query_coverage subject_coverage vf_category gene_description condition
JEJANKPH_00168 VFG002197 BopD 85.1 1.1e-163 1 336 0.9912 1 Biofilm sugar-binding transcriptional regulator, LacI family experiment
JEJANKPH_00168 VFG045671 BopD 89.3 1.4e-168 1 337 0.9941 0.9941 Biofilm sugar-binding transcriptional regulator, LacI family prediction







        Analysis of biocide and heavy metal resistance genes to assess antimicrobial risk and environmental impact


This table presents biocides and heavy metals resistance genes identified within the plasmid cluster.
      Note: Analyzing biocide and heavy metal resistance genes based on BacMet to evaluate bacterial resistance risk and the potential impact of environmental heavy metal contamination. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, E-value < 1e-5) to known biocide and heavy metal resistance genes are listed.

Gene Name compound identity evalue qstart qend query_coverage subject_coverage group






        Analyzing antimicrobial resistance genes to assess bacterial resistance to antibiotics and other antimicrobial agents


This table presents antimicrobial resistance genes identified within the plasmid cluster.
      Note: Antimicrobial resistance was performed using CARD. Genes in plasmid clusters showing strong homology (identity > 70%, coverage > 70%, E-value < 1e-5) to known antimicrobial resistance genes are listed.

Gene Name aro_accession identity evalue qstart qend query_coverage subject_coverage drug_class amr_gene_family resistance_mechanism






Analysis of pathogenicity genes to explore pathogen-host interactions


This table presents host pathogen-host interactions within the plasmid cluster.
      Note: Analyzing pathogenicity-related genes using PHI-base to understand pathogen virulence mechanisms and their impact on host interactions. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e-5) to known pathogenicity-related genes are listed.

Gene Name phi_molconn_id host gene_name identity evalue qstart qend query_coverage subject_coverage host_descripton disease_name function phenotype_of_mutant
JEJANKPH_00029 PHI:5205 HMPREF0351_10118 (WxL locusC) 83.3 8.9e-31 1 72 0.9474 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JEJANKPH_00030 PHI:5205 HMPREF0351_10118 (WxL locusC) 72.5 2.4e-133 4 316 0.9781 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JEJANKPH_00089 PHI:5205 HMPREF0351_10118 (WxL locusC) 89.6 4.4e-206 1 394 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JEJANKPH_00097 PHI:5205 HMPREF0351_10118 (WxL locusC) 71.3 2.8e-165 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JEJANKPH_00142 PHI:5205 HMPREF0351_10118 (WxL locusC) 70.5 2.7e-163 1 389 1.0000 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence
JEJANKPH_00150 PHI:5205 HMPREF0351_10118 (WxL locusC) 78.8 1.1e-183 1 392 0.9899 1.0000 rodents endocarditis involved in bile salt stress and endocarditis pathogenesis reduced virulence






        Analyzing carbohydrate-active enzyme genes to uncover mechanisms of nutrient degradation


This table presents carbohydrate-active enzyme genes identified within the plasmid cluster.
      Note: Annotation of carbohydrate-active enzyme genes was performed using CAZy to explore mechanisms of nutrient breakdown and utilization. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known CAZyme genes are listed.

Gene Name cazy_id identity evalue qstart qend query_coverage subject_coverage
JEJANKPH_00021 QOJ75557.1|GH36 100 0 1 749 1 1
JEJANKPH_00113 QEN53525.1|GH13_18 100 0 1 486 1 1
JEJANKPH_00114 QQJ93880.1|GH13_31 100 1.79e-306 1 406 1 1
JEJANKPH_00115 QAA21152.1|GH36 100 0 1 727 1 1
JEJANKPH_00119 QEN53531.1|GH4 100 0 1 436 1 1
JEJANKPH_00137 QEN53546.1|GH32 100 0 1 479 1 1
JEJANKPH_00165 QAR74517.1|GH65 100 0 1 764 1 1





        Analyzing transport proteins to understand bacterial strategies for substrate uptake and detoxification


This table presents transport proteins within the plasmid cluster.
      Note: Investigation of transport proteins based on TCDB to uncover bacterial mechanisms of substrate transport and environmental detoxification. Genes in plasmid clusters showing strong homology (identity > 70%, subject coverage > 70%, and E-value < 1e−5) to known transport protein entries are listed.

Gene Name tcid identity evalue qstart qend query_coverage subject_coverage class_field class_term subclass subclass_term family family_term
JEJANKPH_00116 3.A.1.1.28 75.3 5.4e-118 5 276 0.9855 0.7294 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily
JEJANKPH_00117 3.A.1.1.28 74.1 2.8e-125 1 290 1.0000 0.7692 3 Primary Active Transporters 3.A P-P-bond-hydrolysis-driven transporters 3.A.1 The ATP-binding Cassette (ABC) Superfamily